FMO DATABASE

FMODB ID: K9J63

Calculation Name: 4L1D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L1D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NY72

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-993122.182009
FMO2-HF: Nuclear repulsion	944907.049028
FMO2-HF: Total energy	-48215.132981
FMO2-MP2: Total energy	-48353.47781

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:VAL)

Summations of interaction energy for fragment #1(A:1:VAL)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-3.133	0.297	0.618	-1.876	-2.172	-0.008

Interaction energy analysis for fragmet #1(A:1:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.012

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	VAL	0	0.042	0.009	2.673	-3.389	-0.023	0.619	-1.872	-2.113	-0.008
4	A	4	GLU	-1	-0.781	-0.876	5.182	-0.564	-0.500	-0.001	-0.004	-0.059	0.000
5	A	5	VAL	0	-0.005	-0.006	8.690	0.065	0.065	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.021	0.010	11.449	0.057	0.057	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.001	0.004	15.150	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.783	-0.862	17.746	-0.536	-0.536	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.033	-0.039	20.541	0.000	0.000	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.793	-0.841	23.657	-0.215	-0.215	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.030	0.011	24.728	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.001	0.001	26.858	0.015	0.015	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.047	0.007	29.520	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.015	-0.002	31.988	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.073	-0.031	26.926	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.006	-0.005	23.689	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	MET	0	-0.003	0.000	21.470	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.829	0.921	13.105	0.744	0.744	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.014	0.013	19.458	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.771	0.842	12.893	0.710	0.710	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.034	0.002	15.223	0.032	0.032	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.000	-0.002	8.586	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.037	-0.004	10.990	0.112	0.112	0.000	0.000	0.000	0.000
24	A	25	MET	0	0.006	0.026	8.007	0.141	0.141	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.865	0.926	8.222	0.345	0.345	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.826	0.906	6.349	-0.135	-0.135	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.815	-0.920	10.681	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.879	-0.932	14.231	0.214	0.214	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.035	-0.033	17.027	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.910	-0.960	18.584	0.049	0.049	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.014	0.029	15.247	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.051	-0.016	16.865	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.040	-0.023	15.998	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.007	0.003	18.562	0.012	0.012	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.039	-0.027	17.812	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.790	-0.875	20.620	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	38	TRP	0	0.014	-0.006	18.592	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.005	-0.010	23.973	0.023	0.023	0.000	0.000	0.000	0.000
39	A	40	TYR	0	0.005	-0.015	26.159	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.844	0.911	28.857	0.179	0.179	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.004	0.018	31.515	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.861	-0.947	34.089	-0.141	-0.141	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.038	-0.020	35.627	0.007	0.007	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.046	-0.008	36.242	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.912	0.932	34.852	0.098	0.098	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.815	-0.886	29.166	-0.169	-0.169	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.028	-0.008	31.381	0.010	0.010	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.001	0.001	26.855	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.021	-0.022	25.901	0.008	0.008	0.000	0.000	0.000	0.000
50	A	51	TYR	0	0.022	-0.019	21.514	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.795	-0.873	24.245	-0.141	-0.141	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.046	-0.011	19.867	0.004	0.004	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.826	0.859	22.481	0.124	0.124	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.019	-0.001	23.702	0.006	0.006	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.061	0.036	23.561	0.013	0.013	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.032	-0.004	18.982	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.023	-0.008	24.067	0.017	0.017	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.894	-0.935	27.426	-0.116	-0.116	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.040	-0.022	28.503	0.005	0.005	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.928	-0.951	31.189	-0.090	-0.090	0.000	0.000	0.000	0.000
61	A	62	SER	0	-0.005	-0.013	31.662	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	63	PRO	0	-0.046	-0.028	34.126	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.002	0.001	29.129	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	GLN	0	0.014	0.003	29.996	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.008	-0.002	30.478	0.006	0.006	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.703	0.812	29.541	0.160	0.160	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.010	0.012	24.810	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.009	0.011	21.210	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.030	0.028	15.414	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.037	-0.031	16.673	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.089	0.056	13.321	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.091	-0.069	9.573	0.036	0.036	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.978	0.963	11.527	0.147	0.147	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.791	-0.855	7.937	-0.574	-0.574	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.020	0.020	11.621	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	GLN	0	0.015	0.011	5.832	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.813	-0.881	9.937	-0.984	-0.984	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.007	-0.021	11.466	0.121	0.121	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.001	-0.027	14.253	0.060	0.060	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.026	0.011	16.720	0.030	0.030	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.048	-0.034	19.993	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	83	VAL	0	0.035	0.025	21.843	0.025	0.025	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.010	-0.017	24.567	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ASN	0	-0.024	-0.020	27.484	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.034	0.041	27.027	0.008	0.008	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.003	-0.014	30.251	0.012	0.012	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.043	0.015	32.884	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.005	-0.013	34.477	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.713	-0.794	29.856	-0.171	-0.171	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.000	0.002	30.222	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.010	0.014	29.912	0.014	0.014	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.056	-0.017	25.498	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.004	-0.020	24.041	0.009	0.009	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.026	-0.022	23.156	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.016	0.010	20.094	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.030	0.012	15.150	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	99	SER	0	0.010	0.007	18.377	0.008	0.008	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.803	0.874	12.131	0.368	0.368	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.916	-0.959	17.954	-0.074	-0.074	0.000	0.000	0.000	0.000
100	A	102	PHE	0	0.008	0.011	17.638	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	110	PHE	0	0.034	0.022	19.756	0.003	0.003	0.000	0.000	0.000	0.000
102	A	111	VAL	0	-0.063	-0.042	15.342	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.839	0.906	18.616	0.188	0.188	0.000	0.000	0.000	0.000
104	A	113	THR	0	-0.056	-0.024	14.271	0.015	0.015	0.000	0.000	0.000	0.000
105	A	114	THR	0	0.011	-0.001	17.460	0.009	0.009	0.000	0.000	0.000	0.000
106	A	115	ARG	1	0.796	0.871	12.705	0.521	0.521	0.000	0.000	0.000	0.000
107	A	116	LEU	0	0.015	0.011	18.660	0.025	0.025	0.000	0.000	0.000	0.000
108	A	117	ILE	0	0.011	0.005	19.390	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	118	PRO	0	-0.010	-0.004	22.734	0.020	0.020	0.000	0.000	0.000	0.000
110	A	119	LEU	0	-0.020	0.010	24.497	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	120	ARG	1	0.881	0.924	26.806	0.231	0.231	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.016	-0.004	28.990	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	122	HIS	0	-0.063	-0.034	29.516	0.024	0.024	0.000	0.000	0.000	0.000
114	A	123	HIS	0	0.022	0.000	32.743	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	124	HIS	0	0.000	0.009	32.036	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:VAL)